Package: soGGi
Type: Package
Title: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate
        plots Summarised Over Grouped Genomic Intervals
Version: 1.41.1
Date: 2025-07-24
Author: Gopuraja Dharmalingam, Doug Barrows, Tom Carroll
Maintainer: Tom Carroll <tc.infomatics@gmail.com>
Description: The soGGi package provides a toolset to create genomic
        interval aggregate/summary plots of signal or motif occurence
        from BAM and bigWig files as well as PWM, rlelist, GRanges and
        GAlignments Bioconductor objects. soGGi allows for
        normalisation, transformation and arithmetic operation on and
        between summary plot objects as well as grouping and subsetting
        of plots by GRanges objects and user supplied metadata. Plots
        are created using the GGplot2 libary to allow user defined
        manipulation of the returned plot object. Coupled together,
        soGGi features a broad set of methods to visualise genomics
        data in the context of groups of genomic intervals such as
        genes, superenhancers and transcription factor binding events.
biocViews: Sequencing, ChIPSeq, Coverage
License: GPL (>= 3)
LazyLoad: yes
Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment
Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, Seqinfo,
        GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
        rtracklayer, preprocessCore, chipseq, BiocParallel
Collate: 'allClasses.r' 'motifTools.R' 'peakTransforms.r' 'plots.R'
        'soggi.R'
VignetteBuilder: knitr
Suggests: testthat, BiocStyle, knitr
NeedsCompilation: no
git_url: https://git.bioconductor.org/packages/soGGi
git_branch: devel
git_last_commit: 827dbf0
git_last_commit_date: 2025-07-24
Repository: Bioconductor 3.22
Date/Publication: 2025-07-25
Packaged: 2025-07-26 02:20:27 UTC; biocbuild
Built: R 4.5.1; ; 2025-07-26 14:11:48 UTC; windows
